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. Author manuscript; available in PMC: 2017 Aug 7.
Published in final edited form as: Nat Biotechnol. 2017 Apr 11;35(4):314–316. doi: 10.1038/nbt.3772

Figure 1.

Figure 1

RNA-seq pipeline and expression concordance. (a) A dependency graph of the RNA-seq pipeline we developed (named CGL). CutAdapt was used to remove extraneous adapters, STAR was used for alignment and read coverage, and RSEM and Kallisto were used to produce quantification data. (b) Scatter plot showing the Pearson correlation between the results of the TCGA best-practices pipeline and the CGL pipeline. 10,000 randomly selected sample and/or gene pairs were subset from the entire TCGA cohort and the normalized counts were plot against each other; this process was repeated five times with no change in Pearson correlation. The unit for counts is: log2(norm_counts+1).